Quite understandably maddening! It would drive me nuts too, even without "real" OCD.
I assume you tried all the usual resets and syncs and etc?
I thought the multiple shelves things was a Kobo server error that they had fixed by now? I recently read in another thread someone with multiple Kobo devices advised to NOT sync several devices in short succession, but to wait a while between syncing devices 1–4. They said that syncing device 1 and then device 2 immediately after would cause shelves to multiply... Do you perhaps have multiple devices? Otherwise, I wouldn't know what to suggest I'm afraid.
As for the download option of deleted books... haven't seen that myself.
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